C6orf15

protein-coding

chromosome 6 open reading frame 15

Gene summary

Predicted to be involved in extracellular matrix organization. Predicted to be active in extracellular matrix. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014070.3

Inheritance

—

ClinVar variants

U:9B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr6:31,111,223-31,112,575

External References & Databases

Ensembl (ENSG00000204542)

Transcript & Mutation Effects

hg38 • Region Span ~1.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C6orf15 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 6

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014070.3. Only rare variants are included.

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			1 clinvar	2 clinvar		3
missense			8 clinvar			8
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	2	0	11

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014070.3	RefSeq	NP_054789.2	2	MANE Select
ENST00000259870.4	Ensembl	ENSP00000259870.3	2	MANE Select
ENST00001140139.1	Ensembl	ENSP00000803015.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component
extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259870
Coding exons: 2
Length: 1337
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125722
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	150	194	0.774	0.0000108	2047
Missense (PolyPhen)		46	58.954	0.78026		607
Synonymous	0.881	66	75.7	0.871	0.00000434	724
Loss of Function	1.18	4	7.47	0.536	4.22e-7	64

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000068	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000082	0.000079	rare
South Asian	0.00036	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.829
RVIS EVS: 1.75
RVIS percentile EVS: 96.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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