Is CEP44 p.Arg82Cys (c.244C>T) pathogenic?

CEP44 p.Arg82Cys (c.244C>T) is classified Uncertain significance in CEP44 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-21). AlphaMissense: likely pathogenic (0.898); Ultra-rare (popmax 0.035%, amr).

How common is CEP44 p.Arg82Cys (c.244C>T) in the general population?

CEP44 p.Arg82Cys (c.244C>T) is ultra-rare (popmax 0.035%, amr) (gnomAD).

What do computational predictors say about CEP44 p.Arg82Cys (c.244C>T)?

AlphaMissense predicts likely pathogenic (score 0.898) — an in-silico prediction, not a clinical call.

CEP44 p.Arg82Cys

c.244C>T · rs368964236 · VCV2346895

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.898 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.035%, amr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.898	likely pathogenic · top 10% in CEP44
REVEL	0.472	indeterminate
SaProt	LLR -7.71	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	Δ0.42	acceptor loss, 6 bp away · masked 0 · deltas
Pangolin	Δ0.41	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 18 kb · p 0.48 · regional, not allelic
Overall
CADD	25.2	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 0.035% Admixed American · 20/57,082 alleles

Filtering AF 0.0232% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0194%

Overall 0.00368% 56/1,521,962 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.035%	2,854
African / African-American	0.0314%	3,189
East Asian	0.00459%	21,779
Remaining individualsnot grpmax-eligible	0.00173%	57,892
Finnishnot grpmax-eligible	0.00162%	61,606
European (non-Finnish)	0.000807%	123,983

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: CEP44
Protein: p.Arg82Cys
Coding: c.244C>T
MANE Select: NM_001040157
dbSNP: rs368964236
Type: single nucleotide variant
Location: chr4:174303709 (GRCh38)
Gene constraint: LOEUF 1.34 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.41 · 1 PDB
Residue 82: the 'binds with microtubules and centrioles' region; an α-helix

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

Similar variants

CEP44 p.Arg82His Uncertain significance ★ ⚠ same residue
CEP44 p.Ala102Gly Uncertain significance ★ ⚠ same type
CEP44 p.Ala155Thr Uncertain significance ★ ⚠ same type
CEP44 p.Ala172Ser Uncertain significance ★ ⚠ same type
CEP44 p.Ala172Thr Uncertain significance ★ ⚠ same type
CEP44 p.Ala172Val Uncertain significance ★ ⚠ same type
CEP44 p.Ala349Gly Uncertain significance ★ ⚠ same type
CEP44 p.Arg11Gln 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-arg82cys (accessed [today's date]).

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