Is CEP44 p.Ala172Ser (c.514G>T) pathogenic?

CEP44 p.Ala172Ser (c.514G>T) is classified Uncertain significance in CEP44 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-14). AlphaMissense: likely benign (0.2767); Absent from gnomAD v4.1.

How common is CEP44 p.Ala172Ser (c.514G>T) in the general population?

CEP44 p.Ala172Ser (c.514G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEP44 p.Ala172Ser (c.514G>T)?

AlphaMissense predicts likely benign (score 0.2767) — an in-silico prediction, not a clinical call.

CEP44 p.Ala172Ser

c.514G>T · rs561221477 · VCV2311838

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2767 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2767	likely benign
REVEL	0.114	moderately benign-leaning
SaProt	LLR -4.91	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 9.3	GERP 2.1, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 18 kb · p 0.48 · regional, not allelic
Overall
CADD	23.3	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: CEP44
Protein: p.Ala172Ser
Coding: c.514G>T
MANE Select: NM_001040157
dbSNP: rs561221477
Type: single nucleotide variant
Location: chr4:174308695 (GRCh38)
Gene constraint: LOEUF 1.34 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.41 · 1 PDB
Residue 172: the 'binds with microtubules and centrioles' region

Full CEP44 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP44 p.Ala172Thr Uncertain significance ★ ⚠ same residue
CEP44 p.Ala172Val Uncertain significance ★ ⚠ same residue
CEP44 p.Ala102Gly Uncertain significance ★ ⚠ same type
CEP44 p.Ala155Thr Uncertain significance ★ ⚠ same type
CEP44 p.Ala349Gly Uncertain significance ★ ⚠ same type
CEP44 p.Arg11Gln Uncertain significance ★ same type
CEP44 p.Arg176Cys Uncertain significance ★ same type
CEP44 p.Arg72His 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/cep44-p-ala172ser (accessed [today's date]).

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