CCDC141

protein-coding

coiled-coil domain containing 141, the group of Immunoglobulin like domain containing

Gene summary

Predicted to be involved in heterophilic cell-cell adhesion and regulation of synapse assembly. Predicted to act upstream of or within centrosome localization and cerebral cortex radially oriented cell migration. Predicted to be located in centrosome and cytoplasm. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173648.4

Inheritance

ClinVar variants

U:310B:105

Top phenotype

Kallmann syndrome

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr2:178,829,757-179,050,137

External References & Databases

Ensembl (ENSG00000163492)

Transcript & Mutation Effects

hg38 • Region Span ~220.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hypogonadotropic hypogonadismLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0018555

Submitter: Ambry Genetics

Kallmann syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018800

Submitter: Orphanet

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CCDC141 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 251

not providedTotal: 225

CCDC141-related disorderTotal: 25

Hypogonadotropic hypogonadism 7 with or without anosmiaTotal: 7

Hypogonadotropic hypogonadismTotal: 2

Disorder of sexual differentiationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173648.4. 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			2 clinvar	60 clinvar	1 clinvar	63
missense			294 clinvar	38 clinvar	4 clinvar	336
nonsense			5 clinvar	2 clinvar		7
start loss						0
frameshift			7 clinvar			7
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	310	100	5	415

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173648.4	RefSeq	NP_775919.3	24	MANE Select
ENST00000443758.7	Ensembl	ENSP00000390190.2	24	MANE Select
NM_001316745.2	RefSeq	NP_001303674.1	12	Standard
ENST00000343876.6	Ensembl	ENSP00000344627.2	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

cytoplasm
microtubule organizing center

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000420890
Coding exons: 24
Length: 220330
Individuals with no LoFs: 125585
Homozygous LoFs: 0
Heterozygous LoFs: 156
Defined: 125741
p: 0.000621

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0354	750	747	1.00	0.0000377	10093
Missense (PolyPhen)		207	214.11	0.9668		3291
Synonymous	0.516	271	282	0.961	0.0000150	2777
Loss of Function	1.57	59	73.5	0.803	0.00000351	976

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00057	0.00043	rare
Latino/Admixed American	0.00035	0.00032	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00094	0.00092	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00038	0.00036	rare
South Asian	0.0025	0.0024	notable
Other	0.00036	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a critical role in radial migration and centrosomal function. {ECO:0000250|UniProtKB:A2AST1}.;

Recessive Scores

pRec: 0.0869

Essentials

Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.557

Gene Damage Prediction

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