OMD

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			55 clinvar	2 clinvar		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	2	0	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005014.3	RefSeq	NP_005005.1	2	MANE Select
ENST00000375550.5	Ensembl	ENSP00000364700.4	2	MANE Select
ENST00000949678.1	Ensembl	ENSP00000619737.1	2	Standard
ENST00000949678.2	Ensembl	ENSP00000619737.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of carbohydrates
Keratan sulfate biosynthesis
Keratan sulfate/keratin metabolism
Glycosaminoglycan metabolism
Metabolism

Biological Process

cell adhesion
keratan sulfate biosynthetic process
regulation of bone mineralization
keratan sulfate catabolic process

Cellular Component

extracellular region
Golgi lumen
lysosomal lumen
collagen-containing extracellular matrix
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375550
Coding exons: 2
Length: 10217
Individuals with no LoFs: 125642
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 125685
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.756	184	215	0.855	0.0000101	2837
Missense (PolyPhen)		63	75.357	0.83602		1013
Synonymous	0.414	71	75.6	0.939	0.00000368	743
Loss of Function	0.872	9	12.3	0.732	6.14e-7	173

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00026	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00082	0.00082	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be implicated in biomineralization processes. Has a function in binding of osteoblasts via the alpha(V)beta(3)- integrin (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.177

Intolerance Scores

LoFtool: 0.597
RVIS EVS: 0.33
RVIS percentile EVS: 73.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.107

Gene Damage Prediction

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