chr17:7578283:G>A Detail (hg19) (TP53)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr17:7,578,283-7,578,283
hg38	chr17:7,674,965-7,674,965 View the variant detail on this assembly version.

HGVS

TP53

Type	Transcript	Protein
RefSeq	NM_000546.5:c.566C>T	NP_000537.3:p.Ala189Val
	NM_001126112.2:c.566C>T	NP_001119584.1:p.Ala189Val
	NM_001276760.1:c.566C>T	NP_001263689.1:p.Ala189Val
	NM_001276761.1:c.566C>T	NP_001263690.1:p.Ala189Val
	NM_001126113.2:c.566C>T	NP_001119585.1:p.Ala189Val
	NM_001276695.1:c.566C>T	NP_001263624.1:p.Ala189Val
	NM_001126116.1:c.170C>T	NP_001119588.1:p.Ala57Val
	NM_001276698.1:c.170C>T	NP_001263627.1:p.Ala57Val
	NM_001126118.1:c.449C>T	NP_001119590.1:p.Ala150Val
	NM_001126117.1:c.89C>T	NP_001119589.1:p.Ala30Val
	NM_001276699.1:c.89C>T	NP_001263628.1:p.Ala30Val
	NM_001126115.1:c.89C>T	NP_001119587.1:p.Ala30Val
	NM_001276697.1:c.89C>T	NP_001263626.1:p.Ala30Val
	NM_001276696.1:c.449C>T	NP_001263625.1:p.Ala150Val
Ensemble	ENST00000604348.6:c.545C>T	ENST00000604348.6:p.Ala182Val
	ENST00000576024.2:c.566C>T	ENST00000576024.2:p.Ala189Val
	ENST00000269305.9:c.566C>T	ENST00000269305.9:p.Ala189Val
	ENST00000714409.1:c.566C>T	ENST00000714409.1:p.Ala189Val
	ENST00000359597.8:c.566C>T	ENST00000359597.8:p.Ala189Val
	ENST00000413465.6:c.566C>T	ENST00000413465.6:p.Ala189Val
	ENST00000420246.6:c.566C>T	ENST00000420246.6:p.Ala189Val
	ENST00000445888.6:c.566C>T	ENST00000445888.6:p.Ala189Val
	ENST00000455263.6:c.566C>T	ENST00000455263.6:p.Ala189Val
	ENST00000504290.5:c.170C>T	ENST00000504290.5:p.Ala57Val
	ENST00000504937.5:c.170C>T	ENST00000504937.5:p.Ala57Val
	ENST00000510385.5:c.170C>T	ENST00000510385.5:p.Ala57Val
	ENST00000610292.4:c.449C>T	ENST00000610292.4:p.Ala150Val
	ENST00000610538.4:c.449C>T	ENST00000610538.4:p.Ala150Val
	ENST00000610623.4:c.89C>T	ENST00000610623.4:p.Ala30Val
	ENST00000618944.4:c.89C>T	ENST00000618944.4:p.Ala30Val
	ENST00000619186.4:c.89C>T	ENST00000619186.4:p.Ala30Val
	ENST00000619485.4:c.449C>T	ENST00000619485.4:p.Ala150Val
	ENST00000620739.4:c.449C>T	ENST00000620739.4:p.Ala150Val
	ENST00000622645.4:c.449C>T	ENST00000622645.4:p.Ala150Val
	ENST00000714356.1:c.449C>T	ENST00000714356.1:p.Ala150Val
	ENST00000714357.1:c.566C>T	ENST00000714357.1:p.Ala189Val
	ENST00000714359.1:c.566C>T	ENST00000714359.1:p.Ala189Val
	ENST00000714408.1:c.566C>T	ENST00000714408.1:p.Ala189Val

Summary

MGeND

Clinical significance	Pathogenic Uncertain significance not provided
Variant entry	134
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.002
	ToMMo:0.002
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:<0.001

Prediction

ClinVar

Clinical Significance	Conflicting classifications of pathogenicity
Review star
Show details

Links

TP53

Type	Database	ID	Link
Gene	MIM	191170	OMIM
	HGNC	11998	HGNC
	Ensembl	ENSG00000141510	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv56957329	TogoVar
	COSMIC	COSM5095506	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute	Citation
not provided		bronchus or lung, unspecified	not provided	MGS000041 (TMGS000094)	Hitoshi Nakagama	National Cancer Center Japan
not provided		fundus of stomach	not provided	MGS000040 (TMGS000095)	Hitoshi Nakagama	National Cancer Center Japan
not provided		pyloric antrum	not provided	MGS000040 (TMGS000095)	Hitoshi Nakagama	National Cancer Center Japan
not provided		descending colon	not provided	MGS000040 (TMGS000095)	Hitoshi Nakagama	National Cancer Center Japan
not provided		malignant neoplasm of rectum	not provided	MGS000040 (TMGS000095)	Hitoshi Nakagama	National Cancer Center Japan
not provided		liver cell carcinoma	not provided	MGS000040 (TMGS000095)	Hitoshi Nakagama	National Cancer Center Japan
not provided		ill-defined sites within the digestive system	not provided	MGS000040 (TMGS000095)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2019/02/13	breast, unspecified	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
not provided		Non-small cell lung cancer	somatic	MGS000026 (TMGS000046)	Manabu Muto	Kyoto University
Uncertain significance	2018/01/13	breast, unspecified	germline	MGS000028 (TMGS000049)	Yukihide Momozawa	RIKEN	30287823
Pathogenic	2021/03/19	control	germline	MGS000047 (TMGS000111)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Uncertain significance	2021/03/19	breast	germline	MGS000048 (TMGS000112)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Pathogenic	2021/03/19	Colorectal	germline	MGS000050 (TMGS000114)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Uncertain significance	2021/03/19	pancreatic	germline	MGS000051 (TMGS000115)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
not provided		other	somatic	MGS000039 (TMGS000092)	Hitoshi Nakagama	National Cancer Center Japan	29659903
not provided		sigmoid colon	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		colon, unspecified	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		body of pancreas	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		ill-defined sites within the digestive system	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		bronchus or lung, unspecified	not provided	MGS000042 (TMGS000093)	Hitoshi Nakagama	National Cancer Center Japan
not provided		oesophagus, unspecified	not provided	MGS000041 (TMGS000094)	Hitoshi Nakagama	National Cancer Center Japan
not provided		fundus of stomach	not provided	MGS000041 (TMGS000094)	Hitoshi Nakagama	National Cancer Center Japan
not provided		malignant neoplasm of rectosigmoid junction	not provided	MGS000041 (TMGS000094)	Hitoshi Nakagama	National Cancer Center Japan
not provided		malignant neoplasm of rectum	not provided	MGS000041 (TMGS000094)	Hitoshi Nakagama	National Cancer Center Japan

Past history: no past history; Family history: no family history; Histological type: NA; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: colorectal and gastric; Histological type: invasive solid-tubular carcinoma; ER: positive; PgR: negative; HER2: negative; (1)
Past history: no past history; Family history: breast and gastric; Histological type: invasive papillotubular carcinoma; ER: positive; PgR: negative; HER2: positive; (1)
Past history: no past history; Family history: bileduct and renal; Histological type: invasive scirrhous carcinoma; ER: positive; PgR: positive; HER2: negative; (1)
Past history: colorectal; Family history: gastric; Histological type: invasive papillotubular carcinoma; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: colorectal and gastric; Histological type: invasive papillotubular carcinoma; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: no family history; Histological type: NA; ER: negative; PgR: negative; HER2: positive; (1)
Past history: no past history; Family history: no family history; Histological type: invasive scirrhous carcinoma; ER: negative; PgR: negative; HER2: positive; (1)
Past history: no past history; Family history: no family history; Histological type: noninvasive ductal carcinoma; ER: negative; PgR: negative; HER2: negative; (1)
Past history: no past history; Family history: no family history; Histological type: invasive scirrhous carcinoma; ER: positive; PgR: positive; HER2: NA; (1)
Past history: no past history; Family history: no family history; Histological type: invasive scirrhous carcinoma; ER: NA; PgR: NA; HER2: NA; (1)
Past history: no past history; Family history: gastric and liver; Histological type: NA; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: breast and pancreatic; Histological type: invasive papillotubular carcinoma; ER: negative; PgR: negative; HER2: equivocal; (1)
Past history: no past history; Family history: no family history; Histological type: invasive papillotubular carcinoma; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: gastric; Histological type: invasive scirrhous carcinoma; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: breast, colorectal, and pancreatic; Histological type: invasive scirrhous carcinoma; ER: positive; PgR: positive; HER2: equivocal; (1)
Past history: no past history; Family history: no family history; Histological type: noninvasive ductal carcinoma; ER: NA; PgR: NA; HER2: NA; (1)
Past history: no past history; Family history: bileduct; Histological type: invasive scirrhous carcinoma; ER: negative; PgR: negative; HER2: negative; (1)
Past history: no past history; Family history: gastric and lung; Histological type: invasive papillotubular carcinoma; ER: NA; PgR: NA; HER2: NA; (1)

Past history: breast; Family history: gastric; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (3)
Past history: prostate; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: gastric; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (5)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: NA; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; Age range: 10-39; (1)
Past history: no past history; Family history: gastric; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (2)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (10)
Past history: no past history; Family history: gastric; Histological type: adenocarcinoma; Anatomic site of CRC: NA; (1)
Past history: gastric; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: right-side colon; (1)
Past history: no past history; Family history: prostate; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: both side of colon; (1)
Past history: no past history; Family history: colorectal; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: no family history; Histological type: others; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: gastric; Family history: no family history; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: breast; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: no past history; Family history: breast, gastric, lung, and renal; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)
Past history: gastric; Family history: gastric, liver, and pancreatic; Histological type: adenocarcinoma; Anatomic site of CRC: NA; (1)
Past history: no past history; Family history: liver; Histological type: adenocarcinoma; Anatomic site of CRC: left-side colon and rectum; (1)

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Pathogenic	2003-02-01	no assertion criteria provided	Familial colorectal cancer	unknown	Detail
Conflicting interpretations of pathogenicity	2021-07-20	criteria provided, conflicting interpretations	Hereditary cancer-predisposing syndrome	germline	Detail
Uncertain significance	2023-04-12	criteria provided, multiple submitters, no conflicts	Li-Fraumeni syndrome 1	germline unknown	Detail
Uncertain significance	2024-01-17	criteria provided, single submitter	Li-Fraumeni syndrome	germline	Detail
Likely benign	2022-03-30	criteria provided, single submitter	hereditary breast ovarian cancer syndrome	germline	Detail
Likely benign	2021-12-08	criteria provided, single submitter	not specified	germline	Detail
Likely benign	2022-12-12	criteria provided, single submitter	not provided	unknown	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.441	Li-Fraumeni syndrome 1	NA	CLINVAR		Detail
0.122	Neoplastic Syndromes, Hereditary	NA	CLINVAR		Detail
0.191	Colonic Neoplasms	Germline TP53 mutation c.566C>T results in the missense mutation GCC (Ala) to...	BeFree	23667851	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Familial colorectal cancer	ClinVar	Detail
NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Li-Fraumeni syndrome 1	ClinVar	Detail
NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Li-Fraumeni syndrome	ClinVar	Detail
NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND Hereditary breast ovarian cancer syndrome	ClinVar	Detail
NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND not specified	ClinVar	Detail
NM_000546.6(TP53):c.566C>T (p.Ala189Val) AND not provided	ClinVar	Detail
NA	DisGeNET	Detail
NA	DisGeNET	Detail
Germline TP53 mutation c.566C>T results in the missense mutation GCC (Ala) to GTC (Val) at codon ...	DisGeNET	Detail

Overlapped Transcript Coordinates

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs121912665 dbSNP
Genome: hg19
Position: chr17:7,578,283-7,578,283
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1210
Mean of sample read depth (HGVD): 99.80
Standard deviation of sample read depth (HGVD): 44.81
Number of reference allele (HGVD): 2416
Number of alternative allele (HGVD): 4
Allele Frequency (HGVD): 0.001652892561983471
Gene Symbol (HGVD): TP53
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs121912665
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0021
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 35
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8652
East Asian Allele Counts (ExAC): 4
East Asian Heterozygous Counts (ExAC): 4
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 4.623208506703652E-4
Chromosome Counts in All Race (ExAC): 121338
Allele Counts in All Race (ExAC): 5
Heterozygous Counts in All Race (ExAC): 5
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 4.120720631624058E-5

Genome browser

chr17:7578283:G>A Detail (hg19) (TP53)

Genome

HGVS

MGeND

Frequency

Prediction

ClinVar

Clinical information of patient(s) with this variant provided by the submitter(s)

Clinical information of patient(s) with this variant provided by the submitter(s)

Clinical information of patient(s) with this variant provided by the submitter(s)

Clinical information of patient(s) with this variant provided by the submitter(s)

Image provided by the submitter

Annotations

Overlapped Transcript Coordinates

Overlapped Transcript