chr1:76269460:G>A Detail (hg19) (MSH4)

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Information

Genome

Assembly	Position
hg19	chr1:76,269,460-76,269,460
hg38	chr1:75,803,775-75,803,775 View the variant detail on this assembly version.

Type	Transcript	Protein
RefSeq	NM_002440.3:c.289G>A	NP_002431.2:p.Ala97Thr
Ensemble	ENST00000263187.4:c.289G>A	ENST00000263187.4:p.Ala97Thr

Summary

Links

Type	Database	ID	Link
Gene	MIM	602105	OMIM
	HGNC	7327	HGNC
	Ensembl	ENSG00000057468	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv2030061	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2023-04-11	criteria provided, single submitter	spermatogenic failure 2	germline	Detail
Benign	2023-04-11	criteria provided, single submitter	Premature ovarian failure 20	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	breast carcinoma	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail
0.004	breast carcinoma	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail
0.013	Malignant neoplasm of breast	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail
0.003	Malignant neoplasm of breast	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail
0.008	breast carcinoma	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail
<0.001	breast carcinoma	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail
<0.001	Malignant neoplasm of breast	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail
0.015	Malignant neoplasm of breast	Using unconditional logistic regression we found that MLH3 (L844P, G>A) polym...	BeFree	19781088	Detail

Annotation

Descrption	Source	Links
NM_002440.4(MSH4):c.289G>A (p.Ala97Thr) AND Spermatogenic failure 2	ClinVar	Detail
NM_002440.4(MSH4):c.289G>A (p.Ala97Thr) AND Premature ovarian failure 20	ClinVar	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro)...	DisGeNET	Detail

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

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
Genome: hg19
Position: chr1:76,269,460-76,269,460
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1210
Mean of sample read depth (HGVD): 63.25
Standard deviation of sample read depth (HGVD): 27.39
Number of reference allele (HGVD): 2297
Number of alternative allele (HGVD): 123
Allele Frequency (HGVD): 0.050826446280991734
Gene Symbol (HGVD): MSH4
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)): rs5745325
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0585
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 980
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8640
East Asian Allele Counts (ExAC): 175
East Asian Heterozygous Counts (ExAC): 171
East Asian Homozygous Counts (ExAC): 2
East Asian Allele Frequency (ExAC): 0.02025462962962963
Chromosome Counts in All Race (ExAC): 120590
Allele Counts in All Race (ExAC): 31769
Heterozygous Counts in All Race (ExAC): 22463
Homozygous Counts in All Race (ExAC): 4653
Allele Frequency in All Race (ExAC): 0.26344638858943525

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