KHDC1

protein-coding

KH domain containing 1

Gene summary

Predicted to enable identical protein binding activity and poly(U) RNA binding activity. Predicted to be located in membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf148
C6orf147

MANE transcript

NM_030568.5

Inheritance

—

ClinVar variants

U:32B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.18

Max pathogenic AF

—

Genomic locus

chr6:73,241,314-73,310,365

External References & Databases

Ensembl (ENSG00000135314)

Transcript & Mutation Effects

hg38 • Region Span ~69.1 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 KHDC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030568.5. 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		1
missense			32 clinvar	4 clinvar		36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	5	0	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030568.5	RefSeq	NP_085045.3	3	MANE Select
ENST00000257765.10	Ensembl	ENSP00000257765.5	3	MANE Select
NM_001251874.4	RefSeq	NP_001238803.2	3	Standard
NM_001395215.3	RefSeq	NP_001382144.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370384
Coding exons: 5
Length: 69052
Individuals with no LoFs: 124782
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 124801
p: 0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.144	129	134	0.965	0.00000737	1534
Missense (PolyPhen)		35	36.883	0.94896		393
Synonymous	0.244	49	51.2	0.957	0.00000312	467
Loss of Function	-0.556	13	11.0	1.18	5.63e-7	108

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.509
RVIS EVS: 0.04
RVIS percentile EVS: 56.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0860

Gene Damage Prediction

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