HMCES

5-hydroxymethylcytosine binding, ES cell specific

Basic information

Region (hg38): 3:129278828-129306186

Previous symbols: [ "C3orf37" ]

Links

ENSG00000183624 ∙ NCBI:56941 ∙ OMIM:618288 ∙ HGNC:24446 ∙ Uniprot:Q96FZ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HMCES gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMCES gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	30	2	1

Variants in HMCES

This is a list of pathogenic ClinVar variants found in the HMCES region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-129279761-C-T		not specified	Uncertain significance (Apr 13, 2022)
3-129279795-G-C		not specified	Uncertain significance (Mar 01, 2024)
3-129279796-G-A		not specified	Uncertain significance (Dec 11, 2023)
3-129279810-G-C		not specified	Uncertain significance (Nov 27, 2023)
3-129279878-A-G		not specified	Likely benign (Nov 10, 2022)
3-129288847-G-A			Benign (Sep 11, 2018)
3-129288873-G-A		not specified	Uncertain significance (Dec 17, 2024)
3-129288884-C-A		not specified	Uncertain significance (May 11, 2022)
3-129288884-C-T		not specified	Uncertain significance (Mar 07, 2025)
3-129288890-C-T		not specified	Uncertain significance (Mar 29, 2024)
3-129288891-G-A		not specified	Uncertain significance (Aug 02, 2023)
3-129288891-G-T		not specified	Uncertain significance (May 14, 2024)
3-129288936-A-T		not specified	Uncertain significance (Dec 15, 2024)
3-129288963-G-A		not specified	Uncertain significance (Feb 22, 2025)
3-129288972-C-T		not specified	Uncertain significance (Mar 11, 2022)
3-129288986-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-129288992-T-G		not specified	Uncertain significance (Jan 29, 2024)
3-129290728-A-G		not specified	Uncertain significance (Jun 16, 2024)
3-129290740-G-A		not specified	Uncertain significance (Jun 22, 2023)
3-129290775-A-G		not specified	Uncertain significance (Jan 17, 2025)
3-129290779-A-G		not specified	Uncertain significance (Nov 10, 2022)
3-129298363-A-C		not specified	Uncertain significance (Dec 17, 2023)
3-129298363-A-G		not specified	Uncertain significance (Nov 09, 2022)
3-129298379-G-A		not specified	Uncertain significance (May 06, 2022)
3-129298390-T-C		not specified	Uncertain significance (Feb 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMCES	protein_coding	protein_coding	ENST00000383463	6	27359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-7	0.686	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0978	200	196	1.02	0.0000101	2307
Missense in Polyphen		65	68.959	0.94259		817
Synonymous	1.22	58	71.0	0.816	0.00000346	676
Loss of Function	1.20	13	18.6	0.700	9.58e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00113
Ashkenazi Jewish	0.00	0.00
East Asian	0.000275	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.000275	0.000272
South Asian	0.000404	0.000392
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically binds 5-hydroxymethylcytosine (5hmC)- containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014). {ECO:0000250, ECO:0000269|PubMed:23945014}.

Intolerance Scores

• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.350
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hmces
• Phenotype: cellular phenotype; growth/size/body region phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: proteolysis;biological_process
• Molecular function: molecular_function;DNA binding;peptidase activity