Is CEP131 p.Arg155= (c.465G>A) pathogenic?

CEP131 p.Arg155= (c.465G>A) is classified Likely benign in CEP131 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-01). Rare (popmax 0.505%, nfe).

How common is CEP131 p.Arg155= (c.465G>A) in the general population?

CEP131 p.Arg155= (c.465G>A) is rare (popmax 0.505%, nfe) (gnomAD).

CEP131 p.Arg155=

c.465G>A · rs142431349 · VCV2648440

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.505%, nfe)

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 1.3	GERP -0.85, phastCons 0.58
Overall
CADD	5.148	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.505% European (non-Finnish) · 5,964/1,180,032 alleles

Filtering AF 0.495% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.49%

Overall 0.42% 6,774/1,614,144 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.939%	106
Remaining individualsnot grpmax-eligible	0.517%	194
European (non-Finnish)grpmax	0.505%	198
Amishnot grpmax-eligible	0.219%	456
Admixed American	0.155%	645
African / African-American	0.104%	962
Finnishnot grpmax-eligible	0.0516%	1,939
Middle Eastern	0.0495%	2,021

Ashkenazi Jewish 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: CEP131
Protein: p.Arg155=
Coding: c.465G>A
MANE Select: NM_014984
dbSNP: rs142431349
Type: single nucleotide variant
Location: chr17:81206794 (GRCh38)
Gene constraint: LOEUF 1.031 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.20
Residue 155: the 'interaction with plk4' region; the 'disordered' region

Full CEP131 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP131 p.Arg155Gln Uncertain significance ★ ⚠ same residue
CEP131 p.Pro365Ser Uncertain significance ★★ ⚠ same type
CEP131 p.Ala1024Thr Uncertain significance ★ ⚠ same type
CEP131 p.Ala1042Ser Uncertain significance ★ ⚠ same type
CEP131 p.Ala113Pro Uncertain significance ★ ⚠ same type
CEP131 p.Ala271Pro Uncertain significance ★ ⚠ same type
CEP131 p.Ala332Ser Uncertain significance ★ ⚠ same type
CEP131 p.Ala403Val 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/cep131-p-arg155 (accessed [today's date]).

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