Is ADNP p.Asp967= (c.2901C>T) pathogenic?

ADNP p.Asp967= (c.2901C>T) is classified Likely benign in ADNP (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-30). Very rare (popmax 0.00439%, sas); Associated with Inborn genetic diseases.

What condition is associated with ADNP p.Asp967= (c.2901C>T)?

ADNP p.Asp967= (c.2901C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ADNP p.Asp967= (c.2901C>T) in the general population?

ADNP p.Asp967= (c.2901C>T) is very rare (popmax 0.00439%, sas) (gnomAD).

ADNP p.Asp967=

c.2901C>T · rs761180077 · VCV1797458

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00439%, sas)

Conditions

Inborn genetic diseases

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 -2.1	GERP -3.8
Overall
CADD	1.382	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00439% South Asian · 4/91,084 alleles

Filtering AF 0.00172% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00149%

Overall 0.0031% 50/1,614,086 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0128%	7,811
Finnishnot grpmax-eligible	0.00937%	10,673
South Asiangrpmax	0.00439%	22,771
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,600
Admixed American	0.00333%	29,998
European (non-Finnish)	0.00246%	40,691

Remaining individuals 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: ADNP
Protein: p.Asp967=
Coding: c.2901C>T
MANE Select: NM_001282531
dbSNP: rs761180077
Type: single nucleotide variant
Location: chr20:50891813 (GRCh38)
Gene constraint: LOEUF 0.106 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 57.07
Residue 967: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ADNP p.Ser738Ter Pathogenic ★★ same condition
ADNP p.Trp446Ter Pathogenic ★★ same condition
ADNP p.Arg264Gln Uncertain significance ★★ ⚠ same condition
ADNP p.Arg296Gln Uncertain significance ★★ ⚠ same condition
ADNP p.Asn331Tyr Uncertain significance ★★ ⚠ same condition
ADNP p.Asn951Ser Uncertain significance ★★ ⚠ same condition
ADNP p.Gln302His Uncertain significance ★★ ⚠ same condition
ADNP p.Glu1024Val 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/adnp-p-asp967 (accessed [today's date]).

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