Is CEP68 p.Val607Ala (c.1820T>C) pathogenic?

CEP68 p.Val607Ala (c.1820T>C) is classified Benign in CEP68 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.0579); Low-frequency (popmax 2.43%, afr).

How common is CEP68 p.Val607Ala (c.1820T>C) in the general population?

CEP68 p.Val607Ala (c.1820T>C) is low-frequency (popmax 2.43%, afr) (gnomAD).

What do computational predictors say about CEP68 p.Val607Ala (c.1820T>C)?

AlphaMissense predicts likely benign (score 0.0579) — an in-silico prediction, not a clinical call.

CEP68 p.Val607Ala

c.1820T>C · rs114749990 · VCV791855

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0579 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.43%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0579	likely benign
REVEL	0.02	moderately benign-leaning
SaProt	LLR -5.62	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 -0.37	GERP -1.9
Regional constraint	o/e 1.01	unconstrained · MANE · 13 kb · p 0.74 · regional, not allelic
Overall
CADD	3.72	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 2.43% African / African-American · 1,825/74,974 alleles

Filtering AF 2.34% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.3%

Overall 0.131% 2,117/1,614,104 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.43%	41
Remaining individualsnot grpmax-eligible	0.186%	539
Admixed American	0.17%	588
Middle Eastern	0.148%	674
South Asian	0.00549%	18,216
European (non-Finnish)	0.00508%	19,667

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: CEP68
Protein: p.Val607Ala
Coding: c.1820T>C
MANE Select: NM_015147
dbSNP: rs114749990
Type: single nucleotide variant
Location: chr2:65072916 (GRCh38)
Gene constraint: LOEUF 0.627 · pLI 0.05 (gnomAD)
Structure: AlphaFold pLDDT 49.36
Residue 607: the 'disordered' region

Full CEP68 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP68 c.2007+9C>G Benign ★★ same type
CEP68 p.Arg217His Benign ★★ ⚠ same type
CEP68 p.His566= Benign/Likely benign ★★ same type
CEP68 p.Phe367Tyr Benign ★★ same type
CEP68 p.Ser447= Benign ★★ same type
CEP68 p.Ala163Thr Uncertain significance ★ ⚠ same type
CEP68 p.Ala214Val Uncertain significance ★ ⚠ same type
CEP68 p.Ala325Val 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/cep68-p-val607ala (accessed [today's date]).

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