Is CCDC71 p.Val455Ile (c.1363G>A) pathogenic?

CCDC71 p.Val455Ile (c.1363G>A) is classified Uncertain significance in CCDC71 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-08). AlphaMissense: likely benign (0.0784); Ultra-rare (popmax 0.0253%, afr).

How common is CCDC71 p.Val455Ile (c.1363G>A) in the general population?

CCDC71 p.Val455Ile (c.1363G>A) is ultra-rare (popmax 0.0253%, afr) (gnomAD).

What do computational predictors say about CCDC71 p.Val455Ile (c.1363G>A)?

AlphaMissense predicts likely benign (score 0.0784) — an in-silico prediction, not a clinical call.

CCDC71 p.Val455Ile

c.1363G>A · rs774180246 · VCV3139333

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0784 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0253%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0784	likely benign
REVEL	0.021	moderately benign-leaning
SaProt	LLR -6.87	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.095	GERP -2.8
Regional constraint	o/e 1.08	unconstrained · MANE · 1,135 bp · p 0.091 · regional, not allelic
Overall
CADD	14.32	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0253% African / African-American · 19/74,960 alleles

Filtering AF 0.0166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0137%

Overall 0.00254% 41/1,613,692 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0253%	3,945
Middle Eastern	0.0165%	6,072
South Asian	0.00988%	10,119
Remaining individualsnot grpmax-eligible	0.0032%	31,228
European (non-Finnish)	0.000847%	117,997

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: CCDC71
Protein: p.Val455Ile
Coding: c.1363G>A
MANE Select: NM_022903
dbSNP: rs774180246
Type: single nucleotide variant
Location: chr3:49162846 (GRCh38)
Gene constraint: LOEUF 1.135 · pLI 0.26 (gnomAD)
Structure: AlphaFold pLDDT 52.59

Full CCDC71 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC71 p.Ala106Pro Uncertain significance ★ ⚠ same type
CCDC71 p.Ala126Thr Uncertain significance ★ ⚠ same type
CCDC71 p.Ala128Val Uncertain significance ★ ⚠ same type
CCDC71 p.Ala132Ser Uncertain significance ★ ⚠ same type
CCDC71 p.Ala181Gly Uncertain significance ★ ⚠ same type
CCDC71 p.Ala246Pro Uncertain significance ★ ⚠ same type
CCDC71 p.Ala281Gly Uncertain significance ★ ⚠ same type
CCDC71 p.Ala283Asp 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/ccdc71-p-val455ile (accessed [today's date]).

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