HEPACAM2

HEPACAM family member 2, the group of V-set domain containing|I-set domain containing

Basic information

Region (hg38): 7:93188534-93226469

Links

ENSG00000188175 ∙ NCBI:253012 ∙ OMIM:614133 ∙ HGNC:27364 ∙ Uniprot:A8MVW5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HEPACAM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEPACAM2 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			29	2	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	29	3	2

Variants in HEPACAM2

This is a list of pathogenic ClinVar variants found in the HEPACAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-93192260-T-C		not specified	Uncertain significance (Dec 08, 2023)
7-93192326-G-A		not specified	Uncertain significance (Jan 29, 2024)
7-93192348-C-A		not specified	Uncertain significance (Feb 07, 2023)
7-93195872-T-A		not specified	Uncertain significance (Jan 31, 2022)
7-93197397-A-C		not specified	Uncertain significance (Feb 28, 2023)
7-93197523-C-T		not specified	Uncertain significance (Nov 01, 2022)
7-93197542-A-C		not specified	Uncertain significance (Jul 06, 2021)
7-93197551-T-A		not specified	Uncertain significance (Jun 13, 2024)
7-93197577-A-G		not specified	Uncertain significance (Sep 25, 2023)
7-93197591-C-G		not specified	Uncertain significance (Jul 08, 2022)
7-93208583-C-T		not specified	Uncertain significance (Aug 23, 2021)
7-93208630-A-G		not specified	Uncertain significance (Nov 14, 2023)
7-93208649-A-C		not specified	Uncertain significance (Jan 29, 2024)
7-93208799-C-A		not specified	Uncertain significance (Apr 25, 2023)
7-93208832-C-A		not specified	Uncertain significance (Dec 27, 2022)
7-93215500-T-C		not specified	Uncertain significance (Dec 19, 2023)
7-93215506-G-A			Benign (Jun 05, 2018)
7-93215520-G-A		not specified	Likely benign (Sep 27, 2022)
7-93215569-G-C		not specified	Uncertain significance (Feb 16, 2023)
7-93215572-A-G		not specified	Uncertain significance (Jan 23, 2023)
7-93215581-C-G		not specified	Uncertain significance (Oct 03, 2022)
7-93215586-C-T		not specified	Uncertain significance (Feb 01, 2023)
7-93215616-G-A		not specified	Uncertain significance (Aug 16, 2021)
7-93215628-A-G		not specified	Uncertain significance (Dec 19, 2022)
7-93215638-C-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEPACAM2	protein_coding	protein_coding	ENST00000394468	10	37939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-10	0.207	125603	1	133	125737	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.252	237	248	0.955	0.0000118	3021
Missense in Polyphen		73	92.593	0.7884		1145
Synonymous	0.368	88	92.5	0.951	0.00000463	904
Loss of Function	0.688	17	20.3	0.835	8.59e-7	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000777	0.000775
Ashkenazi Jewish	0.000401	0.000397
East Asian	0.00110	0.00109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.00110	0.00109
South Asian	0.00186	0.00180
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required during prometaphase for centrosome maturation. Following poly-ADP-ribosylation (PARsylation) by TNKS, translocates from the Golgi apparatus to mitotic centrosomes and plays a key role in the formation of robust microtubules for prompt movement of chromosomes: anchors AKAP9/CG-NAP, a scaffold protein of the gamma-tubulin ring complex and promotes centrosome maturation. {ECO:0000269|PubMed:22864114}.

Recessive Scores

• pRec: 0.0932

Intolerance Scores

• loftool: 0.931
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.229

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hepacam2

Gene ontology

• Biological process: centrosome cycle;cell division
• Cellular component: Golgi membrane;Golgi apparatus;centrosome;spindle;integral component of membrane;midbody
• Molecular function: protein binding