Is CDCA7 p.Asp294Val (c.881A>T) pathogenic?

CDCA7 p.Asp294Val (c.881A>T) is classified Likely benign in CDCA7 (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-28). AlphaMissense: likely benign (0.1346); Rare (popmax 0.364%, eas).

How common is CDCA7 p.Asp294Val (c.881A>T) in the general population?

CDCA7 p.Asp294Val (c.881A>T) is rare (popmax 0.364%, eas) (gnomAD).

What do computational predictors say about CDCA7 p.Asp294Val (c.881A>T)?

AlphaMissense predicts likely benign (score 0.1346) — an in-silico prediction, not a clinical call.

CDCA7 p.Asp294Val

c.881A>T · rs138353896 · VCV797455

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1346 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.364%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1346	likely benign
REVEL	0.13	moderately benign-leaning
SaProt	LLR -6.33	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>G here scores Δ0.35 · evaluated, not missing
Constraint at this position
Conservation	phyloP 5.9	GERP 0.48, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 11 kb · p 0.02 · regional, not allelic
Overall
CADD	19.97	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM D215V vs ClinVar D294V) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.364% East Asian · 160/43,974 alleles

Filtering AF 0.318% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.3%

Overall 0.0127% 200/1,577,766 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.364%	275
Remaining individualsnot grpmax-eligible	0.0311%	3,218
South Asian	0.0211%	4,748
Admixed American	0.002%	50,102
European (non-Finnish)	0.000171%	583,826

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: CDCA7
Protein: p.Asp294Val
Coding: c.881A>T
MANE Select: NM_031942
dbSNP: rs138353896
Type: single nucleotide variant
Location: chr2:173364976 (GRCh38)
Gene constraint: LOEUF 0.676 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.93 · 2 PDB
Residue 294: a UniProt-annotated variant site (in icf3; uncertain significance); a turn

Full CDCA7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDCA7 c.384+2T>C Uncertain significance ★★ same type
CDCA7 p.Ala157Val Uncertain significance ★★ ⚠ same type
CDCA7 p.Ala391Gly Uncertain significance ★★ ⚠ same type
CDCA7 p.Arg134Leu Uncertain significance ★★ ⚠ same type
CDCA7 p.Arg134Trp Uncertain significance ★★ ⚠ same type
CDCA7 p.Arg171Cys Uncertain significance ★★ ⚠ same type
CDCA7 p.Arg171Leu Uncertain significance ★★ ⚠ same type
CDCA7 p.Arg239Gln 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/cdca7-p-asp294val (accessed [today's date]).

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