Is CEP44 p.Ile129= (c.387T>C) pathogenic?

CEP44 p.Ile129= (c.387T>C) is classified Likely benign in CEP44 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-01). Low-frequency (popmax 1.06%, mid).

How common is CEP44 p.Ile129= (c.387T>C) in the general population?

CEP44 p.Ile129= (c.387T>C) is low-frequency (popmax 1.06%, mid) (gnomAD).

CEP44 p.Ile129=

c.387T>C · rs148050333 · VCV2655190

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.06%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -2.2, phastCons 0.024
Overall
CADD	6.617	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.06% Middle Eastern · 63/5,934 alleles

Filtering AF 0.852% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.775%

Overall 0.459% 7,259/1,581,170 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	4.3%	23
Ashkenazi Jewishnot grpmax-eligible	1.12%	89
Middle Easterngrpmax	1.06%	94
European (non-Finnish)	0.516%	194
Remaining individualsnot grpmax-eligible	0.469%	213
Admixed American	0.435%	230
South Asian	0.182%	550
Finnishnot grpmax-eligible	0.122%	817
African / African-American	0.0963%	1,039
East Asian	0.00225%	44,370

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ile129=
Coding: c.387T>C
MANE Select: NM_001040157
dbSNP: rs148050333
Type: single nucleotide variant
Location: chr4:174304249 (GRCh38)
Gene constraint: LOEUF 1.34 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.41 · 1 PDB
Residue 129: 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.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
CEP44 p.Arg176Cys 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-ile129 (accessed [today's date]).

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