HMCN2

hemicentin 2, the group of I-set domain containing|Fibulins

Basic information

Region (hg38): 9:130265760-130434123

Links

ENSG00000148357 ∙ NCBI:256158 ∙ ∙ HGNC:21293 ∙ Uniprot:Q8NDA2 ∙ 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 HMCN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMCN2 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				24		24
missense				1		1
nonsense						0
start loss						0
frameshift				2		2
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				1	1	2
non coding						0
Total	0	0	0	28	0

Variants in HMCN2

This is a list of pathogenic ClinVar variants found in the HMCN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-130286317-A-C			Benign (Jul 01, 2023)
9-130299289-G-A			Likely benign (Jul 01, 2023)
9-130302915-G-C			Likely benign (Jun 01, 2022)
9-130306895-T-C			Likely benign (Sep 01, 2022)
9-130348567-C-T			Likely benign (Nov 01, 2022)
9-130348669-G-A			Likely benign (Jan 01, 2023)
9-130349061-T-C			Likely benign (Jan 01, 2023)
9-130353063-C-G			Likely benign (Sep 01, 2022)
9-130354842-C-T			Likely benign (Sep 01, 2022)
9-130354887-G-A			Likely benign (May 01, 2022)
9-130354932-C-T			Likely benign (Sep 01, 2022)
9-130358452-G-C			Likely benign (Sep 01, 2022)
9-130362950-G-A			Likely benign (Nov 01, 2022)
9-130368356-C-T			Likely benign (Dec 01, 2022)
9-130379397-AC-A			Likely benign (May 01, 2023)
9-130384761-C-T			Likely benign (May 01, 2022)
9-130391304-G-A			Likely benign (Jan 01, 2023)
9-130395332-C-T			Likely benign (Oct 01, 2022)
9-130396251-C-T			Likely benign (Jul 01, 2022)
9-130402790-C-T			Likely benign (Oct 01, 2022)
9-130404882-C-T			Likely benign (Jul 01, 2022)
9-130410582-G-A			Likely benign (Nov 01, 2022)
9-130418919-G-A			Likely benign (Jan 01, 2023)
9-130424807-C-T			Likely benign (Jan 01, 2023)
9-130424860-ACT-A			Likely benign (Jul 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMCN2	protein_coding	protein_coding	ENST00000428715	14	262629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.80e-12	0.586	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	368	430	0.855	0.0000284	5012
Missense in Polyphen		115	142.03	0.8097		1833
Synonymous	1.64	160	189	0.848	0.0000131	1646
Loss of Function	1.49	23	32.1	0.717	0.00000155	375

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.127
• ghis: 0.406

Essentials

• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmcn2

Gene ontology

• Biological process: response to stimulus
• Cellular component: basement membrane;extracellular space;cell cortex;cell junction;extracellular matrix;cleavage furrow;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;calcium ion binding