Is CEP192 p.Ser1412Arg (c.4236C>A) pathogenic?

CEP192 p.Ser1412Arg (c.4236C>A) is classified Uncertain significance in CEP192 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-15). AlphaMissense: likely pathogenic (0.7018); Very rare (popmax 0.00668%, afr).

How common is CEP192 p.Ser1412Arg (c.4236C>A) in the general population?

CEP192 p.Ser1412Arg (c.4236C>A) is very rare (popmax 0.00668%, afr) (gnomAD).

What do computational predictors say about CEP192 p.Ser1412Arg (c.4236C>A)?

AlphaMissense predicts likely pathogenic (score 0.7018) — an in-silico prediction, not a clinical call.

CEP192 p.Ser1412Arg

c.4236C>A · rs765425768 · VCV2249435

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7018 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00668%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7018	likely pathogenic · top 10% in CEP192
REVEL	0.112	moderately benign-leaning
SaProt	LLR -8.16	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.3	GERP -5.1
Regional constraint	o/e 0.96	unconstrained · MANE · 125 kb · p 0.044 · regional, not allelic
Overall
CADD	4.977	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 0.00668% African / African-American · 5/74,886 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.00031% 5/1,613,894 alleles · very rare

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: CEP192
Protein: p.Ser1412Arg
Coding: c.4236C>A
MANE Select: NM_032142
dbSNP: rs765425768
Type: single nucleotide variant
Location: chr18:13057712 (GRCh38)
Gene constraint: LOEUF 0.61 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 51.37 · 6 PDB

Full CEP192 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP192 p.Ala2312Val Uncertain significance ★★ ⚠ same type
CEP192 p.Gly37Val Uncertain significance ★★ ⚠ same type
CEP192 p.Asn1883Ser Benign ★★ same type
CEP192 p.Gly1571= Benign ★★ same type
CEP192 p.Leu111Phe Benign ★★ same type
CEP192 p.Pro1159Arg Benign ★★ same type
CEP192 p.Pro613= Benign ★★ same type
CEP192 p.Thr1053Ala Benign ★★ 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/cep192-p-ser1412arg (accessed [today's date]).

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