Is ANKRD10 p.Ser269Phe (c.806C>T) pathogenic?

ANKRD10 p.Ser269Phe (c.806C>T) is classified Uncertain significance in ANKRD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-13). AlphaMissense: likely benign (0.1211); Absent from gnomAD v4.1.

How common is ANKRD10 p.Ser269Phe (c.806C>T) in the general population?

ANKRD10 p.Ser269Phe (c.806C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ANKRD10 p.Ser269Phe (c.806C>T)?

AlphaMissense predicts likely benign (score 0.1211) — an in-silico prediction, not a clinical call.

ANKRD10 p.Ser269Phe

c.806C>T · VCV3296247

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1211 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1211	likely benign
REVEL	0.303	indeterminate
SaProt	LLR -8.06	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 0.59, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 35 kb · p 0.029 · regional, not allelic
Overall
CADD	22.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ANKRD10
Protein: p.Ser269Phe
Coding: c.806C>T
MANE Select: NM_017664
Type: single nucleotide variant
Location: chr13:110880094 (GRCh38)
Gene constraint: LOEUF 1.035 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.99

Full ANKRD10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKRD10 p.Ala237Val Uncertain significance ★ ⚠ same type
ANKRD10 p.Ala359Thr Uncertain significance ★ ⚠ same type
ANKRD10 p.Ala99Val Uncertain significance ★ ⚠ same type
ANKRD10 p.Asn186Lys Uncertain significance ★ ⚠ same type
ANKRD10 p.Gln106Arg Uncertain significance ★ ⚠ same type
ANKRD10 p.Gln113Glu Uncertain significance ★ ⚠ same type
ANKRD10 p.Gln171Arg Uncertain significance ★ ⚠ same type
ANKRD10 p.Gln199Glu 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/ankrd10-p-ser269phe (accessed [today's date]).

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