Is CDHR1 p.Ala159= (c.477A>G) pathogenic?

CDHR1 p.Ala159= (c.477A>G) is classified Benign in CDHR1 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-03). Common (popmax 69%, afr) — too common for a highly-penetrant pathogenic allele; Associated with cone-rod dystrophy 15.

What condition is associated with CDHR1 p.Ala159= (c.477A>G)?

CDHR1 p.Ala159= (c.477A>G) is associated with cone-rod dystrophy 15 (ClinVar).

How is Cone rod dystrophy inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CDHR1 p.Ala159=

Q: How common is CDHR1 p.Ala159= (c.477A>G) in the general population?

CDHR1 p.Ala159= (c.477A>G) is common (popmax 69%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.477A>G · rs4933975 · VCV262215

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 69%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

cone-rod dystrophy 15

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 -12	GERP -8.9
Overall
CADD	0.016	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 69% African / African-American · 51,680/74,934 alleles

Filtering AF 68.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 68.3%

Overall 46.7% 752,073/1,609,788 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	69%	1
Admixed American	54.7%	2
Remaining individualsnot grpmax-eligible	47.1%	2
Ashkenazi Jewishnot grpmax-eligible	46.6%	2
European (non-Finnish)	45.7%	2
Finnishnot grpmax-eligible	44.9%	2
South Asian	43.7%	2
Middle Eastern	40.9%	2
East Asian	35.1%	3
Amishnot grpmax-eligible	32.5%	3

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: CDHR1
Protein: p.Ala159=
Coding: c.477A>G
MANE Select: NM_033100
dbSNP: rs4933975
Type: single nucleotide variant
Location: chr10:84200639 (GRCh38)
Gene constraint: LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.79
Residue 159: the cadherin 2 domain

Full CDHR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cone-rod dystrophy 15 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Cone rod dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

CDHR1 p.Ala159Glu Likely pathogenic ★ same residue
CDHR1 c.1485+2T>G Pathogenic ★★ same condition
CDHR1 c.525+1G>A Pathogenic ★★ same condition
CDHR1 c.56-1G>A Pathogenic/Likely pathogenic ★★ same condition
CDHR1 c.863-1G>A Pathogenic/Likely pathogenic ★★ same condition
CDHR1 p.Arg407Ter Pathogenic ★★ same condition
CDHR1 c.1554-3C>A Uncertain significance ★★ same condition
CDHR1 c.862+4A>C Uncertain significance ★★ same condition

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/cdhr1-p-ala159 (accessed [today's date]).

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