Is CDC14A p.Ala101Val (c.302C>T) pathogenic?

CDC14A p.Ala101Val (c.302C>T) is classified Uncertain significance in CDC14A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-29). AlphaMissense: ambiguous (0.4907); Very rare (popmax 0.00938%, afr); Associated with Inborn genetic diseases.

What condition is associated with CDC14A p.Ala101Val (c.302C>T)?

CDC14A p.Ala101Val (c.302C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CDC14A p.Ala101Val (c.302C>T) in the general population?

CDC14A p.Ala101Val (c.302C>T) is very rare (popmax 0.00938%, afr) (gnomAD).

What do computational predictors say about CDC14A p.Ala101Val (c.302C>T)?

AlphaMissense predicts ambiguous (score 0.4907) — an in-silico prediction, not a clinical call.

CDC14A p.Ala101Val

c.302C>T · rs140021980 · VCV2602571

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4907 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00938%, afr)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4907	ambiguous
REVEL	0.283	benign-leaning
SaProt	LLR -11.69	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 165 kb · p 0.011 · regional, not allelic
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00938% African / African-American · 7/74,592 alleles

Filtering AF 0.00439% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0031%

Overall 0.000685% 11/1,605,528 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00938%	10,656
Remaining individualsnot grpmax-eligible	0.00161%	62,186
European (non-Finnish)	0.000256%	390,961

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: CDC14A
Protein: p.Ala101Val
Coding: c.302C>T
MANE Select: NM_003672
dbSNP: rs140021980
Type: single nucleotide variant
Location: chr1:100390817 (GRCh38)
Gene constraint: LOEUF 1.141 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.77
Residue 101: the 'a' region

Full CDC14A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDC14A p.Ala101Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
CDC14A p.Ala211Gly Uncertain significance ★★ ⚠ same condition
CDC14A p.Ala482Thr Uncertain significance ★★ ⚠ same condition
CDC14A p.Arg261Gln Uncertain significance ★★ ⚠ same condition
CDC14A p.Arg376Gln Uncertain significance ★★ ⚠ same condition
CDC14A p.Cys12Tyr Uncertain significance ★★ ⚠ same condition
CDC14A p.Glu271Lys Uncertain significance ★★ ⚠ same condition
CDC14A p.Gly283Ala Uncertain significance ★★ ⚠ same condition

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/cdc14a-p-ala101val (accessed [today's date]).

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