Is CCDC141 p.Phe1305= (c.3915C>T) pathogenic?

CCDC141 p.Phe1305= (c.3915C>T) is classified Likely benign in CCDC141 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-28). Very rare (popmax 0.004%, afr).

How common is CCDC141 p.Phe1305= (c.3915C>T) in the general population?

CCDC141 p.Phe1305= (c.3915C>T) is very rare (popmax 0.004%, afr) (gnomAD).

CCDC141 p.Phe1305=

c.3915C>T · VCV3711092

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1	GERP -5.7, phastCons 0.95
Overall
CADD	3.983	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/74,910 alleles

Filtering AF 0.00291% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0026%

Overall 0.00322% 52/1,613,942 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.004%	24,970
European (non-Finnish)	0.00381%	26,222
South Asian	0.0022%	45,538
Admixed American	0.00167%	59,988
Remaining individualsnot grpmax-eligible	0.0016%	62,490

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.Phe1305=
Coding: c.3915C>T
MANE Select: NM_173648
Type: single nucleotide variant
Location: chr2:178837304 (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-phe1305 (accessed [today's date]).

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