Is CCDC141 p.Ala10Val (c.29C>T) pathogenic?

CCDC141 p.Ala10Val (c.29C>T) is classified Benign in CCDC141 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-02). Common (popmax 21.9%, amr) — too common for a highly-penetrant pathogenic allele.

CCDC141 p.Ala10Val

Q: How common is CCDC141 p.Ala10Val (c.29C>T) in the general population?

CCDC141 p.Ala10Val (c.29C>T) is common (popmax 21.9%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.29C>T · rs61397643 · VCV1280772

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 21.9%, amr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.037	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.033	GERP -4.2, phastCons 0.001
Regional constraint	o/e 1.06	unconstrained · MANE · 216 kb · p 0.0073 · regional, not allelic
Overall
CADD	12.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 21.9% Admixed American · 11,156/50,992 alleles

Filtering AF 21.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 21.4%

Overall 10.8% 168,184/1,550,400 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	21.9%	5
Middle Eastern	18.7%	5
South Asian	16.1%	6
East Asian	13.5%	7
African / African-American	12.4%	8
Remaining individualsnot grpmax-eligible	11.2%	9
Ashkenazi Jewishnot grpmax-eligible	10.1%	10
European (non-Finnish)	9.95%	10
Finnishnot grpmax-eligible	6.93%	14
Amishnot grpmax-eligible	6.69%	15

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CCDC141
Protein: p.Ala10Val
Coding: c.29C>T
MANE Select: NM_173648
dbSNP: rs61397643
Type: single nucleotide variant
Location: chr2:179049913 (GRCh38)
Gene constraint: LOEUF 1.052 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.36

Full CCDC141 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC141 p.Ala1261Val Uncertain significance ★★ same type
CCDC141 p.Ala88Thr Uncertain significance ★★ same type
CCDC141 p.Arg1346Trp Uncertain significance ★★ same type
CCDC141 p.Arg1463Ser Uncertain significance ★★ same type
CCDC141 p.Arg1482Trp Uncertain significance ★★ same type
CCDC141 p.Arg180Trp Uncertain significance ★★ same type
CCDC141 p.Arg287Gln Uncertain significance ★★ same type
CCDC141 p.Arg468Gln Uncertain significance ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ccdc141-p-ala10val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown