CCDC91

protein-coding

coiled-coil domain containing 91

Gene summary

Predicted to enable identical protein binding activity. Involved in Golgi to lysosome transport. Located in trans-Golgi network. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018318.5

Inheritance

ClinVar variants

U:54B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr12:28,133,249-28,581,511

External References & Databases

Ensembl (ENSG00000123106)

Transcript & Mutation Effects

hg38 • Region Span ~448.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

punctate palmoplantar keratodermaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0017675

Submitter: G2P

autism spectrum disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005258

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC91 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018318.5. 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						0
missense			52 clinvar	3 clinvar	2 clinvar	57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	54	3	2	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 120 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018318.5	RefSeq	NP_060788.3	12	MANE Select
ENST00000536442.6	Ensembl	ENSP00000445660.2	12	MANE Select
NM_001330367.2	RefSeq	NP_001317296.1	11	Standard
NM_001352078.2	RefSeq	NP_001339007.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
Golgi to lysosome transport

Molecular Function

identical protein binding

Cellular Component

nucleoplasm
Golgi apparatus
trans-Golgi network
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000545336
Coding exons: 12
Length: 446702
Individuals with no LoFs: 125681
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125727
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.431	194	212	0.917	0.00000993	2900
Missense (PolyPhen)		57	69.693	0.81787		1031
Synonymous	-0.878	83	73.4	1.13	0.00000358	771
Loss of Function	2.30	13	25.5	0.509	0.00000115	335

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0011	0.00098	notable
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the regulation of membrane traffic through the trans-Golgi network (TGN). Functions in close cooperation with the GGAs in the sorting of hydrolases to lysosomes. {ECO:0000269|PubMed:17596511}.;

Recessive Scores

pRec: 0.0845

Intolerance Scores

LoFtool: 0.777
RVIS EVS: 1.04
RVIS percentile EVS: 91.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.581

Gene Damage Prediction

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