HMMR

hyaluronan mediated motility receptor, the group of CD molecules

Basic information

Region (hg38): 5:163460203-163491941

Links

ENSG00000072571 ∙ NCBI:3161 ∙ OMIM:600936 ∙ HGNC:5012 ∙ Uniprot:O75330 ∙ 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 HMMR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMMR 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		1	31	4	3	39
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1			1
non coding						0
Total	0	1	33	5	3

Variants in HMMR

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

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

Position	Type	Phenotype	Significance	ClinVar
5-163463895-T-C		not specified	Likely benign (Mar 02, 2023)
5-163463900-G-T		not specified	Uncertain significance (Dec 09, 2023)
5-163463934-A-G		not specified	Uncertain significance (Nov 11, 2024)
5-163463949-A-T		not specified	Uncertain significance (Mar 23, 2022)
5-163464744-T-A		Ovarian cancer	Benign (Jan 01, 2022)
5-163464753-A-T		not specified	Uncertain significance (Mar 14, 2023)
5-163467723-A-C		not specified	Uncertain significance (Apr 13, 2023)
5-163469663-G-A		not specified	Uncertain significance (Feb 27, 2023)
5-163469681-G-A		not specified	Uncertain significance (Oct 13, 2023)
5-163469686-C-G		Familial cancer of breast	Uncertain significance (May 20, 2023)
5-163469773-A-G		not specified	Uncertain significance (Oct 27, 2021)
5-163469814-A-T		not specified	Uncertain significance (Sep 11, 2024)
5-163469819-T-C		Ovarian cancer • not specified	Conflicting classifications of pathogenicity (Jan 16, 2024)
5-163471366-A-G		not specified	Uncertain significance (Mar 20, 2024)
5-163471388-T-C		not specified	Uncertain significance (Feb 27, 2023)
5-163471393-A-G		not specified	Likely benign (Feb 21, 2024)
5-163471423-G-A		not specified	Uncertain significance (May 14, 2024)
5-163471426-G-A		not specified	Uncertain significance (Jul 26, 2022)
5-163471433-A-G		not specified	Uncertain significance (Jan 26, 2023)
5-163473189-G-A		not specified	Uncertain significance (Jul 05, 2024)
5-163473243-G-A		not specified	Uncertain significance (Dec 11, 2023)
5-163473422-C-T		Familial cancer of breast	Uncertain significance (Aug 30, 2022)
5-163473482-G-A		not specified	Uncertain significance (Sep 03, 2024)
5-163473558-G-T		Familial cancer of breast	Uncertain significance (Mar 20, 2019)
5-163474063-A-G		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMMR	protein_coding	protein_coding	ENST00000393915	18	31739

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.52e-21	0.0209	124996	15	736	125747	0.00299

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.550	299	327	0.914	0.0000154	4774
Missense in Polyphen		101	105.25	0.95963		1666
Synonymous	0.815	109	120	0.906	0.00000576	1215
Loss of Function	0.934	35	41.5	0.843	0.00000177	584

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00383	0.00376
Ashkenazi Jewish	0.0552	0.0510
East Asian	0.000451	0.000435
Finnish	0.0000935	0.0000924
European (Non-Finnish)	0.000980	0.000950
Middle Eastern	0.000451	0.000435
South Asian	0.000510	0.000490
Other	0.00670	0.00621

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for hyaluronic acid (HA) (By similarity). Involved in cell motility (By similarity). When hyaluronan binds to HMMR, the phosphorylation of a number of proteins, including PTK2/FAK1 occurs. May also be involved in cellular transformation and metastasis formation, and in regulating extracellular- regulated kinase (ERK) activity. May act as a regulator of adipogenisis (By similarity). {ECO:0000250|UniProtKB:Q00547}.
• Pathway: ECM-receptor interaction - Homo sapiens (human);Hyaluronan uptake and degradation;Hyaluronan metabolism;Metabolism of carbohydrates;Glycosaminoglycan metabolism;Metabolism;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.276

Intolerance Scores

• loftool: 0.998
• rvis_EVS: 2.29
• rvis_percentile_EVS: 98.31

Haploinsufficiency Scores

• pHI: 0.409
• hipred: Y
• hipred_score: 0.566
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.487

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hmmr
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; neoplasm

Gene ontology

• Biological process: regulation of G2/M transition of mitotic cell cycle;hyaluronan catabolic process
• Cellular component: centrosome;cytosol;plasma membrane;cell surface;microtubule cytoskeleton;membrane
• Molecular function: protein binding;hyaluronic acid binding